In the Summer of 1990, Duncan joined the faculty of Reformed Theological Seminary (RTS), Jackson, Mississippi, as the John R. Richardson Chair of Systematic Theology. At the same time he served as assistant pastor of Trinity Presbyterian Church, Jackson, Mississippi (1990–1995), and interim pastor at First Presbyterian Church, Yazoo City, Mississippi (1993).[2]

Effective January 1, 2014, Duncan resigned his position as Sr. Minister at First Presbyterian Church, Jackson, MS, and assumed the role of Chancellor of Reformed Theological Seminary.[2] He continues to teach in the department of Systematic Theology while serving in this role.

Duncan was named senior pastor at First Presbyterian Church of Jackson, Mississippi (PCA) in 1996, and served in that capacity until early 2014. An active churchman, he has been involved in the courts of the Presbyterian Church in America (PCA) in various ways: General Assembly's Committee on Psalmody; Committees of Commissioners for Covenant Theological Seminary, Mission to North America, and Bills and Overtures; member and chair of the Credentials Committee of the Presbytery of the Mississippi Valley (1996–2002); vice-chair of the General Assembly's Creation Study Committee (1998–2000); member of the search committee for a Coordinator of Reformed University Ministries; chair of the General Assembly's Theological Examination Committee; member of the PCA's Strategic Planning Committee; moderator of the Presbytery of the Mississippi Valley (2001); moderator of the PCA General Assembly (2004), making him the youngest elected to this position in the denomination's history.[3]

He is the current president of the Alliance of Confessing Evangelicals,[4] a broad coalition of evangelical Christians from various denominations. It aims to call the church to repent of what it see as its worldliness, and to take up the mantle of the Protestant reformers in recovering the centrality of worship and doctrine in the life of the church. In his capacity as president, Duncan regularly speaks at the Philadelphia Conference on Reformed Theology, an Alliance-related forum that offers quarterly conferences on Reformed doctrine and history.[citation needed] He also contributes to the Alliance's online magazine and blog, Reformation21.[5]

He is also a council member of the Gospel Coalition, a "group of (mostly) pastors and churches in the Reformed heritage who delight in the truth and power of the gospel, and who want the gospel of Christ crucified and resurrected to lie at the center of all we cherish, preach, and teach." They have created The Gospel Coalition Network, which is a consortium of “Christian pastors and other leaders who stimulate one another to faithfulness and fruitfulness in life and ministry in this rapidly-changing, increasingly urbanized, and spiritually hungry world.”[6][better source needed]

Duncan holds to a complementarian view of gender roles.[7][full citation needed] He believes that 1 Corinthians 14:34, which says 'women should keep silent in the churches', refers to women teaching men (like found in 1Timothy 2:12),[8] This puts him at odds with the popular view espoused by Wayne Grudem and Don Carson who insist that the context shows that Paul is prohibiting women from publicly judging prophecy in the church.[9] In the church he serves, men teach mixed adult Sunday school classes, occasionally husband/wife teams teach on issues such as parenting and marriage.[10]